compose.yaml

services:
  autobidsportal:
    build: .
    environment: &idautobidsenv
      DATALAD_SSH_IDENTITYFILE: "/ssh/id_rsa"
      SQLALCHEMY_DATABASE_URI: postgresql+psycopg2://postgres:example@postgres:5432
      SQLALCHEMY_TRACK_MODIFICATIONS: "false"
      REDIS_URL: "redis://redis:6379"
      FLASK_APP: bids_form.py
      AUTOBIDS_SECRET_KEY: secret
      AUTOBIDS_LOG_LEVEL: INFO
      AUTOBIDS_ROOT_URL: autobidsportal
      AUTOBIDS_CFMM2TAR_DOWNLOAD_DIR: /cfmm2tar-download
      AUTOBIDS_TAR2BIDS_DOWNLOAD_DIR: /datasets
      AUTOBIDS_TAR2BIDS_TEMP_DIR: /tmp
      AUTOBIDS_HEURISTIC_REPO_PATH: /home
      AUTOBIDS_CFMM2TAR_PATH: "/opt/apptainer-images/cfmm2tar_v1.1.1.sif"
      AUTOBIDS_CFMM2TAR_BINDS: "/cfmm2tar-download:/cfmm2tar-download,/tmp:/tmp"
      AUTOBIDS_CFMM2TAR_TIMEOUT: "100000"
      AUTOBIDS_TAR2BIDS_PATH: "/opt/apptainer-images/tar2bids_v0.2.0.sif"
      AUTOBIDS_TAR2BIDS_BINDS: "/cfmm2tar-download:/cfmm2tar-download,/datasets:/datasets,/tmp:/tmp,/home:/home"
      AUTOBIDS_TAR2BIDS_TIMEOUT: "100000"
      AUTOBIDS_GRADCORRECT_PATH: "/opt/apptainer-images/gradcorrect_v0.0.3a.sif"
      AUTOBIDS_GRADCORRECT_BINDS: "/cfmm2tar-download:/cfmm2tar-download,/tmp:/tmp,/datasets:/datasets,/appdata:/appdata"
      AUTOBIDS_GRADCORRECT_COEFF_FILE: '/appdata/coeff.grad'
      AUTOBIDS_GRADCORRECT_TIMEOUT: '100000'
      AUTOBIDS_HEURISTIC_DIR_PATH: /home
      AUTOBIDS_DATALAD_RIA_URL: "ria+ssh://user@ria:2222/ria-store"
      AUTOBIDS_ARCHIVE_BASE_URL: "user@archive:/archive"
      AUTOBIDS_ARCHIVE_SSH_PORT: "2222"
      AUTOBIDS_ARCHIVE_SSH_KEY: "/ssh/id_rsa"
      AUTOBIDS_ARCHIVE_TIMEOUT: "100000"
      AUTOBIDS_MAIL_ENABLED: "false"
      AUTOBIDS_DICOM_SERVER_URL: "ORTHANC@orthanc:4242"
      AUTOBIDS_DICOM_SERVER_USERNAME: "user"
      AUTOBIDS_DICOM_SERVER_PASSWORD: "password"
      AUTOBIDS_DICOM_SERVER_TLS: "true"
      AUTOBIDS_DICOM_SERVER_STUDYINSTANCEUID_WILDCARD: "false"
      GIT_AUTHOR_NAME: "Autobids Portal"
      GIT_AUTHOR_EMAIL: "autobids@example.com"
      GIT_COMMITER_NAME: "Autobids Portal"
      GIT_COMMITER_EMAIL: "autobids@example.com"
    ports: ["5000:5000"]
    volumes: &idautobidsvolumes
      - "./compose/cfmm2tar-download:/cfmm2tar-download"
      - "./compose/tar-files:/tar-files"
      - "./compose/ria-store:/ria-store"
      - "./compose/datasets:/datasets"
      - "./compose/ssh:/ssh"
      - "./compose/appdata:/appdata"
    devices:
      - "/dev/fuse:/dev/fuse"
    cap_add:
      - SYS_ADMIN
    privileged: true
    depends_on:
      - postgres
      - redis
      - rq
  rq:
    build: .
    command: rq worker
    environment: *idautobidsenv
    volumes: *idautobidsvolumes
    devices:
      - "/dev/fuse:/dev/fuse"
    cap_add:
      - SYS_ADMIN
    privileged: true
    depends_on:
      - postgres
      - redis
    restart: on-failure
  redis:
    image: redis:5.0.14
    ports: ["6379:6379"]
  postgres:
    image: postgres:11
    restart: unless-stopped
    environment:
      POSTGRES_PASSWORD: example
    volumes:
      - "./compose/postgres-db:/var/lib/postgresql/data"
    ports: ["5432:5432"]
  orthanc:
    image: jodogne/orthanc:1.10.1
    command: /run/secrets/
    secrets:
      - orthanc.json
    ports: ["4242:4242", "8042:8042"]
    volumes:
      - "./compose/orthanc-key.pem:/certs/orthanc.key"
      - "./compose/orthanc-crt.pem:/certs/orthanc.crt"
      - "./compose/dcm4che-crt.pem:/certs/cert.pem"
      - "./compose/orthanc-db:/var/lib/orthanc/db"
  ria:
    image: lscr.io/linuxserver/openssh-server
    hostname: ria
    environment:
      PUBLIC_KEY_FILE: "/ssh/id_rsa.pub"
      SUDO_ACCESS: "true"
      USER_NAME: user
      PUID: 1001
      PGID: 1001
      DOCKER_MODS: linuxserver/mods:openssh-server-git
    ports: ["2222:2222"]
    volumes:
      - "./compose/ria-store-ssh:/ria-store"
      - "./compose/ria-store-custom:/ria-store-custom"
      - "./compose/ssh:/ssh"
  archive:
    image: lscr.io/linuxserver/openssh-server
    hostname: archive
    environment:
      PUBLIC_KEY_FILE: "/ssh/id_rsa.pub"
      SUDO_ACCESS: "true"
      USER_NAME: user
      PUID: 1001
      PGID: 1001
    volumes:
      - "./compose/archive:/archive"
      - "./compose/ssh:/ssh"
  nginx:
    image: nginx:latest
    hostname: nginx
    volumes:
      - "./compose/nginx.conf:/etc/nginx/nginx.conf"
    ports: ["5001:80"]
    depends_on:
      - autobidsportal
secrets:
  orthanc.json:
    file: compose/orthanc.json